Introduction

Data from Sophie’s samples (human cells)

Volcano plot

Getting some stats yay

table(res_tbl$padj<=0.05) # significant genes
## 
## FALSE  TRUE 
## 10761  5551
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange<=-1) # signif and downreg
## 
## FALSE  TRUE 
## 18059   721
table(res_tbl$padj<=0.05&res_tbl$log2FoldChange>=1) # signif and upreg
## 
## FALSE  TRUE 
## 17946   955

GSEA analysis

Gene set enrichment analysis using - pval < 0,05 - pval < 0,001

Filtering on pval < 0,05

Gene ontology (Biological process and Molecular function)

ID setSize NES p.adjust qvalue
GOBP_SENSORY_PERCEPTION_OF_SMELL 14 -2.604039 0.0000072 0.0000063
GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_STIMULUS 449 1.929584 0.0000218 0.0000189
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II 390 1.859271 0.0002490 0.0002162
GOBP_REGULATION_OF_CELLULAR_COMPONENT_MOVEMENT 260 2.023275 0.0002875 0.0002496
GOBP_SENSORY_PERCEPTION 103 -2.330712 0.0002948 0.0002559
GOBP_NEGATIVE_REGULATION_OF_SIGNALING 388 1.830149 0.0004265 0.0003703
GOBP_DETECTION_OF_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION 20 -2.418768 0.0009137 0.0007933
GOBP_NERVOUS_SYSTEM_PROCESS 213 -2.106216 0.0009137 0.0007933
GOBP_DETECTION_OF_STIMULUS 38 -2.453341 0.0010062 0.0008736
GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 226 1.923200 0.0010748 0.0009332
GOBP_POSITIVE_REGULATION_OF_LOCOMOTION 151 2.093809 0.0012865 0.0011169
GOBP_REGULATION_OF_VASCULATURE_DEVELOPMENT 75 2.239023 0.0014072 0.0012217
GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS 22 -2.421340 0.0014957 0.0012985
GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 244 1.871503 0.0015126 0.0013132
GOBP_CELLULAR_RESPONSE_TO_ENDOGENOUS_STIMULUS 375 1.764720 0.0015126 0.0013132
GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_MORPHOGENESIS 226 1.872278 0.0017350 0.0015063
GOBP_CARDIAC_MUSCLE_CELL_PROLIFERATION 13 2.319503 0.0017560 0.0015245
GOBP_CARDIAC_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 10 2.293977 0.0017560 0.0015245
GOBP_STRIATED_MUSCLE_CELL_PROLIFERATION 16 2.337177 0.0029957 0.0026008
GOBP_RESPONSE_TO_ENDOGENOUS_STIMULUS 446 1.629485 0.0040879 0.0035490
GOBP_CELL_MIGRATION 361 1.694351 0.0044389 0.0038538
GOBP_RESPONSE_TO_PURINE_CONTAINING_COMPOUND 30 2.286489 0.0050651 0.0043974
GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION 58 2.133457 0.0050651 0.0043974
GOBP_INFLAMMATORY_RESPONSE 197 1.869834 0.0050651 0.0043974
GOBP_RESPONSE_TO_HORMONE 252 1.819960 0.0050651 0.0043974
GOBP_LOCOMOTION 445 1.612518 0.0050651 0.0043974
GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS 179 1.894588 0.0051440 0.0044659
GOBP_RESPONSE_TO_GROWTH_FACTOR 193 1.862017 0.0051440 0.0044659
GOBP_RESPONSE_TO_STEROID_HORMONE 97 2.043743 0.0051563 0.0044765
GOBP_TISSUE_DEVELOPMENT 464 1.601369 0.0051563 0.0044765
GOBP_RESPONSE_TO_ORGANIC_CYCLIC_COMPOUND 250 1.794170 0.0056766 0.0049283
GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 442 1.639358 0.0058025 0.0050376
GOBP_RESPONSE_TO_LIPID 241 1.810103 0.0058378 0.0050682
GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 14 2.260621 0.0060210 0.0052273
GOBP_NEGATIVE_REGULATION_OF_CELL_DIFFERENTIATION 161 1.897573 0.0060210 0.0052273
GOBP_CYTOKINE_PRODUCTION 210 1.823301 0.0060210 0.0052273
GOBP_TRANSMEMBRANE_TRANSPORT 368 -1.683901 0.0064097 0.0055647
GOBP_BLOOD_VESSEL_MORPHOGENESIS 150 1.894404 0.0071274 0.0061878
GOBP_VASCULATURE_DEVELOPMENT 179 1.852547 0.0071274 0.0061878
GOBP_MATERNAL_PLACENTA_DEVELOPMENT 14 2.243884 0.0072902 0.0063291
GOBP_RESPONSE_TO_LEUKEMIA_INHIBITORY_FACTOR 32 2.182906 0.0080171 0.0069603
GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY 38 -2.156904 0.0082786 0.0071872
GOBP_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS 259 1.710916 0.0082786 0.0071872
GOBP_RESPONSE_TO_BMP 37 2.114334 0.0089636 0.0077819
GOBP_TISSUE_MIGRATION 79 2.069218 0.0089636 0.0077819
GOBP_REGULATION_OF_CELL_DEATH 489 1.528277 0.0097257 0.0084436
GOBP_ENDOTHELIAL_CELL_MIGRATION 58 2.043752 0.0098770 0.0085750
GOBP_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN 91 1.981008 0.0101160 0.0087825
GOBP_OXIDATIVE_PHOSPHORYLATION 81 -2.052380 0.0101222 0.0087878
GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS 77 2.003424 0.0104653 0.0090857
GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION 102 1.972729 0.0104653 0.0090857
GOBP_TUBE_DEVELOPMENT 261 1.712302 0.0104653 0.0090857
GOBP_REGULATION_OF_MULTICELLULAR_ORGANISMAL_DEVELOPMENT 348 1.629821 0.0104653 0.0090857
GOBP_REGULATION_OF_CELL_DIFFERENTIATION 386 1.607020 0.0104653 0.0090857
GOBP_RESPONSE_TO_CAMP 18 2.212699 0.0113149 0.0098233
GOBP_INTRACELLULAR_RECEPTOR_SIGNALING_PATHWAY 88 1.938250 0.0133152 0.0115599
GOBP_TUBE_MORPHOGENESIS 212 1.741479 0.0133152 0.0115599
GOBP_REGULATION_OF_CELL_POPULATION_PROLIFERATION 440 1.561554 0.0133152 0.0115599
GOBP_NEURON_PROJECTION_GUIDANCE 35 -2.175450 0.0137225 0.0119135
GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY 59 -2.066936 0.0137225 0.0119135
GOBP_POSITIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT 41 2.059890 0.0137225 0.0119135
GOBP_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION 130 1.864805 0.0137225 0.0119135
GOBP_INORGANIC_ION_TRANSMEMBRANE_TRANSPORT 202 -1.777687 0.0137225 0.0119135
GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 318 1.625889 0.0139540 0.0121145
GOBP_NEGATIVE_REGULATION_OF_MAP_KINASE_ACTIVITY 27 2.140814 0.0150498 0.0130658
GOBP_TISSUE_REGENERATION 20 2.131696 0.0150498 0.0130658
GOBP_LEUKOCYTE_CHEMOTAXIS 48 2.064539 0.0150498 0.0130658
GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_CELL_MIGRATION 44 2.031502 0.0150498 0.0130658
GOBP_PROTEIN_LOCALIZATION_TO_EXTRACELLULAR_REGION 94 1.939277 0.0150498 0.0130658
GOBP_REGULATION_OF_PROTEIN_SECRETION 63 1.936925 0.0150498 0.0130658
GOBP_GROWTH 277 1.668465 0.0150498 0.0130658
GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT 272 1.643786 0.0153826 0.0133548
GOBP_MATERNAL_PROCESS_INVOLVED_IN_FEMALE_PREGNANCY 19 2.117945 0.0158033 0.0137200
GOBP_ATP_BIOSYNTHETIC_PROCESS 27 -2.116982 0.0158999 0.0138039
GOBP_PHOSPHOLIPASE_C_ACTIVATING_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 12 2.100979 0.0158999 0.0138039
GOBP_POSITIVE_REGULATION_OF_SIGNALING 466 1.505051 0.0163440 0.0141894
GOBP_ION_TRANSPORT 365 -1.621609 0.0169247 0.0146936
GOBP_HOMEOSTATIC_PROCESS 486 1.458519 0.0177165 0.0153810
GOBP_MITOCHONDRIAL_ELECTRON_TRANSPORT_NADH_TO_UBIQUINONE 34 -2.100867 0.0177837 0.0154394
GOBP_NEUTROPHIL_CHEMOTAXIS 21 2.127063 0.0184240 0.0159952
GOBP_ION_TRANSMEMBRANE_TRANSPORT 267 -1.714485 0.0184240 0.0159952
GOBP_REGULATION_OF_ENDOTHELIAL_CELL_MIGRATION 45 2.027747 0.0186452 0.0161873
GOBP_GRANULOCYTE_CHEMOTAXIS 26 2.064060 0.0188227 0.0163414
GOBP_CELLULAR_RESPONSE_TO_CAMP 14 2.114685 0.0194876 0.0169186
GOBP_GRANULOCYTE_MIGRATION 32 2.020678 0.0194876 0.0169186
GOBP_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 49 1.977686 0.0194876 0.0169186
GOBP_CELLULAR_RESPONSE_TO_STEROID_HORMONE_STIMULUS 68 1.925401 0.0194876 0.0169186
GOBP_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 134 -1.801225 0.0194876 0.0169186
GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 369 1.537165 0.0194876 0.0169186
GOBP_NEGATIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION 195 1.724688 0.0201575 0.0175002
GOBP_DEVELOPMENTAL_GROWTH 171 1.705632 0.0201995 0.0175367
GOBP_POSITIVE_REGULATION_OF_PROTEIN_SECRETION 35 2.026529 0.0206373 0.0179168
GOBP_RESPONSE_TO_FIBROBLAST_GROWTH_FACTOR 26 2.035942 0.0208099 0.0180666
GOBP_RESPONSE_TO_MECHANICAL_STIMULUS 50 1.990490 0.0208099 0.0180666
GOBP_CELL_FATE_SPECIFICATION 14 -2.058121 0.0219911 0.0190921
GOBP_INSULIN_SECRETION_INVOLVED_IN_CELLULAR_RESPONSE_TO_GLUCOSE_STIMULUS 16 2.106438 0.0220611 0.0191529
GOBP_REGULATION_OF_LEUKOCYTE_CHEMOTAXIS 26 2.022610 0.0220611 0.0191529
GOBP_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 28 2.067590 0.0220754 0.0191653
GOBP_TRANSFORMING_GROWTH_FACTOR_BETA_RECEPTOR_SIGNALING_PATHWAY 64 1.926464 0.0225810 0.0196043
GOBP_POSITIVE_REGULATION_OF_MIRNA_TRANSCRIPTION 15 2.075249 0.0233102 0.0202373
GOBP_DEFENSE_RESPONSE_TO_GRAM_NEGATIVE_BACTERIUM 17 -2.072162 0.0233216 0.0202472
GOBP_RESPONSE_TO_CORTICOSTEROID 38 2.005354 0.0244370 0.0212156
GOBP_MUSCLE_CELL_PROLIFERATION 45 1.989396 0.0244370 0.0212156
GOBP_RESPONSE_TO_KETONE 50 1.967607 0.0244370 0.0212156
GOBP_MUSCLE_STRUCTURE_DEVELOPMENT 166 1.679903 0.0244370 0.0212156
GOBP_NEGATIVE_REGULATION_OF_LOCOMOTION 81 1.846947 0.0247284 0.0214685
GOBP_NEURON_DEVELOPMENT 290 -1.645452 0.0263569 0.0228824
GOBP_MESENCHYME_DEVELOPMENT 70 1.843632 0.0264506 0.0229637
GOBP_EMBRYONIC_ORGAN_DEVELOPMENT 96 1.856386 0.0274905 0.0238666
GOBP_REGULATION_OF_IMMUNE_SYSTEM_PROCESS 385 1.508617 0.0274905 0.0238666
GOBP_NEUTROPHIL_MIGRATION 26 1.987493 0.0282883 0.0245592
GOBP_REGULATION_OF_GRANULOCYTE_CHEMOTAXIS 10 2.032485 0.0285848 0.0248166
GOBP_CELLULAR_RESPONSE_TO_CORTICOSTEROID_STIMULUS 20 2.025745 0.0301681 0.0261911
GOBP_ENDOTHELIAL_CELL_APOPTOTIC_PROCESS 19 2.015734 0.0306730 0.0266295
GOBP_CELLULAR_RESPONSE_TO_LIPID 158 1.732132 0.0306730 0.0266295
GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS 48 1.956066 0.0308717 0.0268020
GOBP_REGULATION_OF_RESPONSE_TO_STRESS 428 1.489237 0.0327539 0.0284361
GOBP_MUSCLE_TISSUE_DEVELOPMENT 100 1.802422 0.0373395 0.0324172
GOBP_EPIDERMIS_DEVELOPMENT 74 1.864494 0.0381844 0.0331507
GOBP_CELLULAR_RESPONSE_TO_KETONE 32 1.923417 0.0394290 0.0342312
GOBP_PROTON_TRANSMEMBRANE_TRANSPORT 62 -1.908784 0.0394290 0.0342312
GOBP_CELLULAR_RESPONSE_TO_ORGANIC_CYCLIC_COMPOUND 166 1.612745 0.0395728 0.0343561
GOBP_EXPORT_FROM_CELL 207 1.588162 0.0437252 0.0379610
GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION 118 1.724846 0.0492623 0.0427682

ID setSize NES p.adjust qvalue
GOMF_GATED_CHANNEL_ACTIVITY 45 -2.722206 0.0000087 0.0000080
GOMF_PASSIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 78 -2.505033 0.0000087 0.0000080
GOMF_TRANSPORTER_ACTIVITY 311 -2.094972 0.0000087 0.0000080
GOMF_INORGANIC_MOLECULAR_ENTITY_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 159 -2.145919 0.0002807 0.0002573
GOMF_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 193 -2.039061 0.0003346 0.0003067
GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME 110 -2.151438 0.0006879 0.0006306
GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY 114 2.086975 0.0006879 0.0006306
GOMF_CATION_CHANNEL_ACTIVITY 55 -2.345008 0.0010142 0.0009297
GOMF_STRUCTURAL_MOLECULE_ACTIVITY 205 -1.940196 0.0011552 0.0010589
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H_QUINONE_OR_SIMILAR_COMPOUND_AS_ACCEPTOR 35 -2.341321 0.0022323 0.0020463
GOMF_NADH_DEHYDROGENASE_ACTIVITY 31 -2.305218 0.0022323 0.0020463
GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT 20 -2.316265 0.0024774 0.0022709
GOMF_VOLTAGE_GATED_CHANNEL_ACTIVITY 24 -2.270734 0.0027055 0.0024801
GOMF_MOLECULAR_TRANSDUCER_ACTIVITY 161 -1.934640 0.0027055 0.0024801
GOMF_OXIDOREDUCTION_DRIVEN_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 47 -2.259474 0.0027773 0.0025459
GOMF_VOLTAGE_GATED_CATION_CHANNEL_ACTIVITY 13 -2.224729 0.0028445 0.0026075
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H 40 -2.237231 0.0035795 0.0032812
GOMF_CATION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 145 -1.924899 0.0050534 0.0046323
GOMF_CALMODULIN_BINDING 53 -2.089502 0.0069635 0.0063832
GOMF_METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 75 -2.026250 0.0077500 0.0071042
GOMF_LIGAND_GATED_ION_CHANNEL_ACTIVITY 22 -2.149288 0.0082194 0.0075345
GOMF_G_PROTEIN_COUPLED_RECEPTOR_ACTIVITY 56 -2.050913 0.0129778 0.0118963
GOMF_POTASSIUM_CHANNEL_ACTIVITY 11 -2.065129 0.0167877 0.0153887
GOMF_CALCIUM_ION_BINDING 123 -1.804922 0.0222617 0.0204066
GOMF_PRIMARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 74 -1.823311 0.0380247 0.0348560
GOMF_SEQUENCE_SPECIFIC_DNA_BINDING 468 1.446433 0.0380247 0.0348560

Reactome and Wikipathways

ID setSize NES p.adjust qvalue
REACTOME_ANTIMICROBIAL_PEPTIDES 11 -2.416493 0.0000352 0.0000345
REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION 52 -2.280567 0.0082333 0.0080533
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS 85 -2.137745 0.0165632 0.0162012
REACTOME_COMPLEX_I_BIOGENESIS 39 -2.175214 0.0216863 0.0212124
REACTOME_COLLAGEN_BIOSYNTHESIS_AND_MODIFYING_ENZYMES 14 -2.177601 0.0338810 0.0331406
REACTOME_COLLAGEN_FORMATION 17 -2.143959 0.0403484 0.0394666

ID setSize NES p.adjust qvalue
WP_OXIDATIVE_PHOSPHORYLATION 42 -2.432459 0.0013838 0.0012206
WP_ELECTRON_TRANSPORT_CHAIN_OXPHOS_SYSTEM_IN_MITOCHONDRIA 72 -2.190281 0.0080174 0.0070716
WP_NEOVASCULARISATION_PROCESSES 11 2.178213 0.0106192 0.0093663
WP_GLUCOCORTICOID_RECEPTOR_PATHWAY 30 2.142475 0.0106192 0.0093663
WP_MITOCHONDRIAL_COMPLEX_I_ASSEMBLY_MODEL_OXPHOS_SYSTEM 39 -2.119005 0.0106192 0.0093663
WP_VEGFAVEGFR2_SIGNALING_PATHWAY 199 1.732304 0.0106192 0.0093663
WP_HEPATITIS_B_INFECTION 63 1.988885 0.0189726 0.0167342
WP_ANTIVIRAL_AND_ANTIINFLAMMATORY_EFFECTS_OF_NRF2_ON_SARSCOV2_PATHWAY 12 2.104886 0.0218276 0.0192524
WP_NUCLEAR_RECEPTORS_METAPATHWAY 99 1.884068 0.0218276 0.0192524
WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586 32 2.009530 0.0251488 0.0221818
WP_SARSCOV2_INNATE_IMMUNITY_EVASION_AND_CELLSPECIFIC_IMMUNE_RESPONSE 16 2.010436 0.0430691 0.0379879
WP_PREIMPLANTATION_EMBRYO 11 1.997753 0.0430691 0.0379879

Filtering on pval < 0,001

Gene ontology (Biological process and Molecular function)

ID setSize NES p.adjust qvalue
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II 254 2.457021 0.0000008 0.0000006
GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_STIMULUS 279 2.284457 0.0000267 0.0000211
GOBP_TISSUE_DEVELOPMENT 275 2.236483 0.0000267 0.0000211
GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY 37 -3.058197 0.0000338 0.0000266
GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 134 2.462525 0.0000338 0.0000266
GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 144 2.448070 0.0000338 0.0000266
GOBP_RESPONSE_TO_ENDOGENOUS_STIMULUS 269 2.148553 0.0000865 0.0000682
GOBP_NEGATIVE_REGULATION_OF_CELL_DIFFERENTIATION 93 2.519234 0.0000893 0.0000705
GOBP_RESPONSE_TO_MECHANICAL_STIMULUS 29 2.682104 0.0001499 0.0001183
GOBP_NEGATIVE_REGULATION_OF_SIGNALING 241 2.161762 0.0001706 0.0001346
GOBP_OXIDATIVE_PHOSPHORYLATION 64 -2.648267 0.0001748 0.0001379
GOBP_RESPONSE_TO_GROWTH_FACTOR 117 2.348734 0.0001748 0.0001379
GOBP_POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 388 2.008098 0.0001748 0.0001379
GOBP_POSITIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS 439 1.952257 0.0001748 0.0001379
GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY 25 -2.847777 0.0001927 0.0001521
GOBP_CELLULAR_RESPONSE_TO_ENDOGENOUS_STIMULUS 231 2.148787 0.0002535 0.0002000
GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_MORPHOGENESIS 137 2.278341 0.0002982 0.0002353
GOBP_TUBE_DEVELOPMENT 150 2.252512 0.0003245 0.0002560
GOBP_REGULATION_OF_MULTICELLULAR_ORGANISMAL_DEVELOPMENT 203 2.128797 0.0003342 0.0002637
GOBP_REGULATION_OF_CELL_POPULATION_PROLIFERATION 272 2.029179 0.0003342 0.0002637
GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 197 2.165111 0.0003393 0.0002677
GOBP_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 16 2.510212 0.0003880 0.0003061
GOBP_LOCOMOTION 253 2.067096 0.0004413 0.0003482
GOBP_HOMEOSTATIC_PROCESS 292 2.012246 0.0004413 0.0003482
GOBP_REGULATION_OF_CELLULAR_COMPONENT_MOVEMENT 160 2.213417 0.0004862 0.0003836
GOBP_TUBE_MORPHOGENESIS 117 2.248920 0.0004967 0.0003918
GOBP_REGULATION_OF_CELL_DIFFERENTIATION 233 2.030844 0.0007505 0.0005921
GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 271 1.983926 0.0008758 0.0006910
GOBP_NEUROGENESIS 237 1.996374 0.0009515 0.0007507
GOBP_CELL_MIGRATION 208 2.049016 0.0011040 0.0008710
GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT 163 2.077277 0.0011053 0.0008720
GOBP_CARDIAC_MUSCLE_CELL_PROLIFERATION 10 2.372932 0.0012034 0.0009494
GOBP_RESPONSE_TO_ABIOTIC_STIMULUS 213 2.009826 0.0013519 0.0010666
GOBP_VASCULATURE_DEVELOPMENT 107 2.236282 0.0014683 0.0011584
GOBP_EPIDERMAL_CELL_DIFFERENTIATION 25 2.431408 0.0014749 0.0011636
GOBP_STRIATED_MUSCLE_CELL_PROLIFERATION 13 2.393133 0.0015121 0.0011930
GOBP_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS 141 2.097410 0.0015121 0.0011930
GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 225 1.983671 0.0015121 0.0011930
GOBP_ATP_BIOSYNTHETIC_PROCESS 21 -2.522712 0.0023498 0.0018539
GOBP_POSITIVE_REGULATION_OF_CELLULAR_BIOSYNTHETIC_PROCESS 429 1.792270 0.0023498 0.0018539
GOBP_NEURON_DIFFERENTIATION 201 1.990172 0.0024029 0.0018958
GOBP_SKELETAL_SYSTEM_DEVELOPMENT 65 2.244240 0.0026395 0.0020825
GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 100 2.179565 0.0026395 0.0020825
GOBP_RESPONSE_TO_HORMONE 157 2.063305 0.0026395 0.0020825
GOBP_MITOCHONDRIAL_ELECTRON_TRANSPORT_NADH_TO_UBIQUINONE 26 -2.529590 0.0032517 0.0025655
GOBP_RESPIRATORY_ELECTRON_TRANSPORT_CHAIN 47 -2.289075 0.0040044 0.0031593
GOBP_ANIMAL_ORGAN_MORPHOGENESIS 114 2.072108 0.0040044 0.0031593
GOBP_ATP_SYNTHESIS_COUPLED_ELECTRON_TRANSPORT 45 -2.346542 0.0049669 0.0039186
GOBP_ELECTRON_TRANSPORT_CHAIN 56 -2.333223 0.0049669 0.0039186
GOBP_CAMERA_TYPE_EYE_DEVELOPMENT 45 2.223420 0.0055455 0.0043752
GOBP_NEGATIVE_REGULATION_OF_MAP_KINASE_ACTIVITY 18 2.329912 0.0055590 0.0043858
GOBP_BLOOD_VESSEL_MORPHOGENESIS 91 2.108160 0.0058404 0.0046079
GOBP_MESENCHYMAL_CELL_DIFFERENTIATION 34 2.237728 0.0061217 0.0048297
GOBP_RESPONSE_TO_PURINE_CONTAINING_COMPOUND 16 2.272731 0.0062683 0.0049454
GOBP_NEGATIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION 121 2.027320 0.0066089 0.0052142
GOBP_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 29 2.299972 0.0067901 0.0053571
GOBP_ATP_SYNTHESIS_COUPLED_PROTON_TRANSPORT 13 -2.317202 0.0068096 0.0053724
GOBP_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY 57 2.197304 0.0068675 0.0054182
GOBP_DEVELOPMENTAL_GROWTH 110 2.034831 0.0076157 0.0060085
GOBP_NUCLEOSIDE_TRIPHOSPHATE_BIOSYNTHETIC_PROCESS 30 -2.329544 0.0081928 0.0064638
GOBP_RESPONSE_TO_FIBROBLAST_GROWTH_FACTOR 19 2.241322 0.0085622 0.0067552
GOBP_RESPONSE_TO_OXYGEN_LEVELS 63 2.098544 0.0085622 0.0067552
GOBP_NEGATIVE_REGULATION_OF_LOCOMOTION 51 2.164564 0.0096556 0.0076179
GOBP_AEROBIC_RESPIRATION 77 -2.125256 0.0098415 0.0077645
GOBP_EMBRYONIC_ORGAN_DEVELOPMENT 55 2.119014 0.0098494 0.0077708
GOBP_RESPONSE_TO_LIPID 134 1.944070 0.0098564 0.0077763
GOBP_RIBONUCLEOSIDE_TRIPHOSPHATE_METABOLIC_PROCESS 32 -2.316863 0.0107256 0.0084620
GOBP_SENSORY_ORGAN_MORPHOGENESIS 28 2.278581 0.0107256 0.0084620
GOBP_ADENYLATE_CYCLASE_MODULATING_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 20 2.216234 0.0107256 0.0084620
GOBP_EMBRYONIC_MORPHOGENESIS 85 2.023220 0.0107256 0.0084620
GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 54 2.112190 0.0111095 0.0087649
GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS 32 2.171257 0.0114465 0.0090308
GOBP_RHYTHMIC_PROCESS 51 2.134794 0.0114465 0.0090308
GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION 74 2.061603 0.0114465 0.0090308
GOBP_RIBONUCLEOSIDE_TRIPHOSPHATE_BIOSYNTHETIC_PROCESS 29 -2.361446 0.0115075 0.0090789
GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT 14 2.191860 0.0115075 0.0090789
GOBP_MESENCHYME_DEVELOPMENT 39 2.187010 0.0115075 0.0090789
GOBP_TRANSFORMING_GROWTH_FACTOR_BETA_RECEPTOR_SIGNALING_PATHWAY 35 2.123161 0.0115075 0.0090789
GOBP_INFLAMMATORY_RESPONSE 107 2.020555 0.0115075 0.0090789
GOBP_BIOLOGICAL_ADHESION 175 1.844718 0.0115075 0.0090789
GOBP_ADENYLATE_CYCLASE_ACTIVATING_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 13 2.174923 0.0130184 0.0102709
GOBP_RESPONSE_TO_ORGANIC_CYCLIC_COMPOUND 150 1.924459 0.0130184 0.0102709
GOBP_CYTOCHROME_COMPLEX_ASSEMBLY 13 -2.217064 0.0133335 0.0105196
GOBP_MORPHOGENESIS_OF_A_BRANCHING_STRUCTURE 20 2.176893 0.0133409 0.0105254
GOBP_CHEMICAL_HOMEOSTASIS 179 1.855274 0.0139790 0.0110289
GOBP_REGULATION_OF_VASCULATURE_DEVELOPMENT 47 2.114343 0.0139816 0.0110309
GOBP_REGULATION_OF_IMMUNE_SYSTEM_PROCESS 228 1.760676 0.0139816 0.0110309
GOBP_SENSORY_ORGAN_DEVELOPMENT 70 2.076031 0.0140503 0.0110850
GOBP_EXPORT_FROM_CELL 124 1.913804 0.0143056 0.0112865
GOBP_HOMEOSTASIS_OF_NUMBER_OF_CELLS 62 2.069664 0.0144477 0.0113986
GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_VIA_DEATH_DOMAIN_RECEPTORS 20 2.150462 0.0146955 0.0115941
GOBP_REGULATION_OF_CELL_DEATH 306 1.756754 0.0146955 0.0115941
GOBP_REGULATION_OF_CELL_ADHESION 116 1.908772 0.0153883 0.0121407
GOBP_HEART_GROWTH 16 2.133024 0.0156370 0.0123369
GOBP_ENDOTHELIAL_CELL_APOPTOTIC_PROCESS 12 2.118619 0.0156370 0.0123369
GOBP_EPIDERMIS_DEVELOPMENT 44 2.095777 0.0156370 0.0123369
GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS 115 1.952485 0.0156370 0.0123369
GOBP_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN 43 2.067215 0.0158973 0.0125423
GOBP_GROWTH 175 1.802069 0.0158973 0.0125423
GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS 46 2.091458 0.0163778 0.0129214
GOBP_PROTON_TRANSMEMBRANE_TRANSPORT 39 -2.108023 0.0167593 0.0132224
GOBP_EPITHELIAL_CELL_DIFFERENTIATION 94 1.927618 0.0168255 0.0132746
GOBP_CELLULAR_RESPIRATION 82 -2.005384 0.0171230 0.0135093
GOBP_IMMUNE_SYSTEM_DEVELOPMENT 180 1.767938 0.0171767 0.0135517
GOBP_POSITIVE_REGULATION_OF_LOCOMOTION 94 1.900456 0.0207496 0.0163706
GOBP_DEFENSE_RESPONSE_TO_GRAM_NEGATIVE_BACTERIUM 11 -2.223246 0.0209281 0.0165114
GOBP_CELLULAR_RESPONSE_TO_KETONE 20 2.096691 0.0214635 0.0169338
GOBP_REGIONALIZATION 39 2.068977 0.0214635 0.0169338
GOBP_CYTOKINE_PRODUCTION 126 1.894348 0.0214635 0.0169338
GOBP_RESPONSE_TO_CAMP 11 2.058877 0.0225297 0.0177749
GOBP_SENSORY_SYSTEM_DEVELOPMENT 53 2.041380 0.0226019 0.0178319
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS 39 2.055959 0.0227282 0.0179316
GOBP_INTRACELLULAR_RECEPTOR_SIGNALING_PATHWAY 50 2.053141 0.0228639 0.0180386
GOBP_EPITHELIUM_DEVELOPMENT 159 1.834185 0.0232388 0.0183344
GOBP_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION 333 1.631406 0.0240709 0.0189909
GOBP_REGULATION_OF_LEUKOCYTE_CHEMOTAXIS 19 2.065050 0.0249561 0.0196893
GOBP_NEURON_DEVELOPMENT 160 1.803507 0.0249561 0.0196893
GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA 44 2.039957 0.0253374 0.0199901
GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE 40 2.056382 0.0264017 0.0208298
GOBP_PATTERN_SPECIFICATION_PROCESS 51 2.016379 0.0270716 0.0213583
GOBP_NEGATIVE_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS 15 2.022966 0.0279726 0.0220691
GOBP_CELL_CELL_SIGNALING 204 1.713399 0.0288796 0.0227848
GOBP_NUCLEOSIDE_TRIPHOSPHATE_METABOLIC_PROCESS 35 -2.145032 0.0290952 0.0229549
GOBP_LEUKOCYTE_HOMEOSTASIS 19 2.031926 0.0300296 0.0236920
GOBP_MITOCHONDRIAL_TRANSLATION 28 -2.153952 0.0314673 0.0248264
GOBP_PATTERN_RECOGNITION_RECEPTOR_SIGNALING_PATHWAY 36 2.002859 0.0321402 0.0253573
GOBP_REGULATION_OF_EPITHELIAL_CELL_APOPTOTIC_PROCESS 17 2.066857 0.0322741 0.0254629
GOBP_REGULATION_OF_HEART_GROWTH 12 2.028399 0.0322741 0.0254629
GOBP_ATP_METABOLIC_PROCESS 91 -1.977307 0.0328156 0.0258901
GOBP_CONNECTIVE_TISSUE_DEVELOPMENT 37 2.058157 0.0331431 0.0261485
GOBP_MULTI_MULTICELLULAR_ORGANISM_PROCESS 32 1.999619 0.0331431 0.0261485
GOBP_RESPONSE_TO_NITROGEN_COMPOUND 213 1.699730 0.0340649 0.0268758
GOBP_REGULATION_OF_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_VIA_DEATH_DOMAIN_RECEPTORS 14 2.040740 0.0352226 0.0277891
GOBP_POSITIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT 26 2.039691 0.0360148 0.0284141
GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION 23 2.025104 0.0363706 0.0286948
GOBP_RETINA_DEVELOPMENT_IN_CAMERA_TYPE_EYE 18 2.081100 0.0372410 0.0293815
GOBP_MATERNAL_PLACENTA_DEVELOPMENT 10 2.001191 0.0372410 0.0293815
GOBP_CELL_MORPHOGENESIS 154 1.755610 0.0376459 0.0297010
GOBP_MUSCLE_CELL_PROLIFERATION 36 1.970601 0.0384788 0.0303581
GOBP_RESPONSE_TO_STEROID_HORMONE 59 1.950172 0.0384788 0.0303581
GOBP_MATERNAL_PROCESS_INVOLVED_IN_FEMALE_PREGNANCY 13 2.008132 0.0393505 0.0310458
GOBP_PLACENTA_DEVELOPMENT 27 1.999498 0.0393505 0.0310458
GOBP_SULFUR_COMPOUND_BIOSYNTHETIC_PROCESS 34 1.974925 0.0393505 0.0310458
GOBP_MITOCHONDRIAL_ATP_SYNTHESIS_COUPLED_PROTON_TRANSPORT 10 -2.148456 0.0393984 0.0310837
GOBP_CELLULAR_RESPONSE_TO_STEROID_HORMONE_STIMULUS 42 1.996336 0.0393984 0.0310837
GOBP_EYE_MORPHOGENESIS 20 1.992658 0.0393984 0.0310837
GOBP_RECEPTOR_MEDIATED_ENDOCYTOSIS 44 1.970763 0.0393984 0.0310837
GOBP_REGULATION_OF_ORGAN_GROWTH 17 1.953771 0.0393984 0.0310837
GOBP_MUSCLE_TISSUE_DEVELOPMENT 66 1.909303 0.0393984 0.0310837
GOBP_DICARBOXYLIC_ACID_METABOLIC_PROCESS 21 1.990288 0.0396561 0.0312869
GOBP_NEGATIVE_REGULATION_OF_PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY 34 1.944833 0.0396561 0.0312869
GOBP_CELLULAR_RESPONSE_TO_CHEMICAL_STRESS 75 1.905193 0.0396561 0.0312869
GOBP_FORMATION_OF_PRIMARY_GERM_LAYER 14 1.991396 0.0402474 0.0317535
GOBP_MYELOID_CELL_HOMEOSTASIS 42 1.934260 0.0402474 0.0317535
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 194 1.667811 0.0402474 0.0317535
GOBP_CAMERA_TYPE_EYE_MORPHOGENESIS 17 1.944979 0.0431860 0.0340719
GOBP_REGULATION_OF_SECRETION 85 1.871521 0.0431860 0.0340719
GOBP_MITOCHONDRION_ORGANIZATION 155 -1.626760 0.0434095 0.0342482
GOBP_TISSUE_MORPHOGENESIS 74 1.902908 0.0446767 0.0352480
GOBP_CELLULAR_RESPONSE_TO_ALCOHOL 14 1.967098 0.0451459 0.0356182
GOBP_TISSUE_REMODELING 19 1.971774 0.0455033 0.0359001
GOBP_EPITHELIAL_CELL_APOPTOTIC_PROCESS 26 1.993013 0.0464340 0.0366344
GOBP_NEGATIVE_REGULATION_OF_NEURON_DIFFERENTIATION 14 1.964644 0.0464340 0.0366344
GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY 43 1.913018 0.0464340 0.0366344
GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY 55 1.865320 0.0464340 0.0366344
GOBP_REGENERATION 27 1.928821 0.0465573 0.0367317
GOBP_CIRCADIAN_RHYTHM 40 1.919541 0.0479845 0.0378577
GOBP_POSITIVE_REGULATION_OF_CELL_DEATH 107 1.776629 0.0494123 0.0389842
GOBP_CELL_CELL_ADHESION 107 1.771984 0.0494123 0.0389842
GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT 81 1.853856 0.0496882 0.0392019
GOBP_MUCOPOLYSACCHARIDE_METABOLIC_PROCESS 13 1.939632 0.0497603 0.0392587
GOBP_INSULIN_SECRETION_INVOLVED_IN_CELLULAR_RESPONSE_TO_GLUCOSE_STIMULUS 13 1.937878 0.0497603 0.0392587

ID setSize NES p.adjust qvalue
GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME 87 -3.387282 0.0000000 0.0000000
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H_QUINONE_OR_SIMILAR_COMPOUND_AS_ACCEPTOR 26 -2.950293 0.0000243 0.0000209
GOMF_OXIDOREDUCTION_DRIVEN_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 35 -2.877268 0.0000311 0.0000268
GOMF_NADH_DEHYDROGENASE_ACTIVITY 23 -2.831990 0.0001776 0.0001530
GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY 74 2.412904 0.0001776 0.0001530
GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING 173 2.182237 0.0001776 0.0001530
GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY 183 2.164475 0.0001776 0.0001530
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H 30 -2.753930 0.0001800 0.0001551
GOMF_SEQUENCE_SPECIFIC_DNA_BINDING 276 2.046593 0.0001800 0.0001551
GOMF_ELECTRON_TRANSFER_ACTIVITY 49 -2.594089 0.0003521 0.0003033
GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY 304 1.954948 0.0003521 0.0003033
GOMF_STRUCTURAL_MOLECULE_ACTIVITY 136 -2.226044 0.0004210 0.0003627
GOMF_TRANSPORTER_ACTIVITY 167 -1.962410 0.0014546 0.0012532
GOMF_PRIMARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 48 -2.275777 0.0082735 0.0071279
GOMF_PASSIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 33 -2.026467 0.0351792 0.0303079
GOMF_KINASE_BINDING 180 1.745293 0.0476930 0.0410889

Reactome and Wikipathways

ID setSize NES p.adjust qvalue
REACTOME_TRANSLATION 133 -2.636206 0.0000057 0.0000052
REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION 54 -2.767540 0.0001538 0.0001423
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS 63 -2.711163 0.0001538 0.0001423
REACTOME_INFLUENZA_INFECTION 72 -2.517822 0.0002163 0.0002002
REACTOME_REGULATION_OF_EXPRESSION_OF_SLITS_AND_ROBOS 85 -2.516039 0.0002167 0.0002006
REACTOME_MITOCHONDRIAL_TRANSLATION 41 -2.771394 0.0002305 0.0002133
REACTOME_COMPLEX_I_BIOGENESIS 27 -2.759535 0.0002305 0.0002133
REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 62 -2.550541 0.0002305 0.0002133
REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY 57 -2.433269 0.0010015 0.0009268
REACTOME_CELLULAR_RESPONSE_TO_STARVATION 73 -2.330032 0.0029225 0.0027045
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT 51 -2.414203 0.0030033 0.0027793
REACTOME_RRNA_PROCESSING 102 -2.167609 0.0030033 0.0027793
REACTOME_THE_CITRIC_ACID_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT 77 -2.252786 0.0033264 0.0030782
REACTOME_SELENOAMINO_ACID_METABOLISM 58 -2.255485 0.0074161 0.0068628
REACTOME_EUKARYOTIC_TRANSLATION_INITIATION 65 -2.236839 0.0077476 0.0071696
REACTOME_NONSENSE_MEDIATED_DECAY_NMD 64 -2.140318 0.0094670 0.0087607
REACTOME_TOLL_LIKE_RECEPTOR_CASCADES 30 2.209072 0.0108511 0.0100415
REACTOME_SIGNALING_BY_ROBO_RECEPTORS 94 -2.047394 0.0116495 0.0107803

ID setSize NES p.adjust qvalue
WP_OXIDATIVE_PHOSPHORYLATION 34 -3.032978 0.0000070 0.0000056
WP_ELECTRON_TRANSPORT_CHAIN_OXPHOS_SYSTEM_IN_MITOCHONDRIA 57 -2.836425 0.0000070 0.0000056
WP_MITOCHONDRIAL_COMPLEX_I_ASSEMBLY_MODEL_OXPHOS_SYSTEM 27 -2.735064 0.0003258 0.0002629
WP_CYTOPLASMIC_RIBOSOMAL_PROTEINS 53 -2.623085 0.0003258 0.0002629
WP_SUDDEN_INFANT_DEATH_SYNDROME_SIDS_SUSCEPTIBILITY_PATHWAYS 27 2.553020 0.0003258 0.0002629
WP_GLUCOCORTICOID_RECEPTOR_PATHWAY 19 2.254725 0.0106467 0.0085904
WP_CIRCADIAN_RHYTHM_GENES 41 2.154513 0.0106467 0.0085904
WP_OREXIN_RECEPTOR_PATHWAY 24 2.177890 0.0204809 0.0165253
WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586 27 2.166997 0.0204809 0.0165253
WP_HEPATITIS_B_INFECTION 40 2.018225 0.0338204 0.0272884
WP_NEOVASCULARISATION_PROCESSES 10 2.036257 0.0342356 0.0276234
WP_NUCLEAR_RECEPTORS_METAPATHWAY 66 1.975659 0.0350283 0.0282631
WP_VEGFAVEGFR2_SIGNALING_PATHWAY 133 1.838130 0.0350283 0.0282631
WP_BASE_EXCISION_REPAIR 13 -2.086275 0.0478118 0.0385776
WP_COMPLEMENT_SYSTEM_IN_NEURONAL_DEVELOPMENT_AND_PLASTICITY 14 2.021052 0.0478118 0.0385776
WP_IL1_SIGNALING_PATHWAY 17 1.993349 0.0478118 0.0385776

Test specific targets

  • Ajouter les genes sets concernant :
  1. la machinerie UPR
  2. les familles d’oxydo-réduction (enzymes NOX, TXN, reduction du glutathion…)
  3. Machinerie de presentation (CRT, TAP; proteasome…)

The antigen presenting pathway (GO:0019882)

Highlight on the volcano plot of the genes found to be implicated in the endoplasmic reticulum unfolded protein response + table

gene log2FoldChange padj description
RAB8B 1.3082949 0.0000000 RAB8B, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:30273]
TAPBP -0.7495563 0.0000000 TAP binding protein [Source:HGNC Symbol;Acc:HGNC:11566]
RAB35 0.9675892 0.0000000 RAB35, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9774]
LNPEP 1.1727759 0.0000000 leucyl and cystinyl aminopeptidase [Source:HGNC Symbol;Acc:HGNC:6656]
ARL8B 0.7914131 0.0000000 ADP ribosylation factor like GTPase 8B [Source:HGNC Symbol;Acc:HGNC:25564]
PIKFYVE 0.8594568 0.0000001 phosphoinositide kinase, FYVE-type zinc finger containing [Source:HGNC Symbol;Acc:HGNC:23785]
B2M 0.8496441 0.0000001 beta-2-microglobulin [Source:HGNC Symbol;Acc:HGNC:914]
HLA-A -0.8742236 0.0000003 major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:HGNC:4931]
CTSD -0.6241187 0.0000027 cathepsin D [Source:HGNC Symbol;Acc:HGNC:2529]
ERAP2 -0.8017025 0.0000048 endoplasmic reticulum aminopeptidase 2 [Source:HGNC Symbol;Acc:HGNC:29499]
RAB33A 1.3929028 0.0000133 RAB33A, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9773]
RAB6A 0.5461231 0.0000417 RAB6A, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9786]
MICA -0.6871788 0.0000464 MHC class I polypeptide-related sequence A [Source:HGNC Symbol;Acc:HGNC:7090]
FCGR1A -1.0134651 0.0001062 Fc gamma receptor Ia [Source:HGNC Symbol;Acc:HGNC:3613]
AP3B1 0.7257227 0.0002469 adaptor related protein complex 3 subunit beta 1 [Source:HGNC Symbol;Acc:HGNC:566]
HLA-B 0.5741303 0.0002662 major histocompatibility complex, class I, B [Source:HGNC Symbol;Acc:HGNC:4932]
WDFY4 0.7758152 0.0002878 WDFY family member 4 [Source:HGNC Symbol;Acc:HGNC:29323]
ERAP1 0.5559485 0.0005007 endoplasmic reticulum aminopeptidase 1 [Source:HGNC Symbol;Acc:HGNC:18173]
MARCHF1 1.0198236 0.0005036 membrane associated ring-CH-type finger 1 [Source:HGNC Symbol;Acc:HGNC:26077]

The endoplasmic reticulum unfolded protein response GO:0030968

Highlight on the volcano plot of the genes found to be implicated in the endoplasmic reticulum unfolded protein response + table

gene log2FoldChange padj description
PIK3R1 1.7581776 0.0000000 phosphoinositide-3-kinase regulatory subunit 1 [Source:HGNC Symbol;Acc:HGNC:8979]
EIF2A 1.3500520 0.0000000 eukaryotic translation initiation factor 2A [Source:HGNC Symbol;Acc:HGNC:3254]
CREBRF 3.1055803 0.0000000 CREB3 regulatory factor [Source:HGNC Symbol;Acc:HGNC:24050]
PARP6 -1.1134644 0.0000000 poly(ADP-ribose) polymerase family member 6 [Source:HGNC Symbol;Acc:HGNC:26921]
ERLEC1 1.0245015 0.0000000 endoplasmic reticulum lectin 1 [Source:HGNC Symbol;Acc:HGNC:25222]
PTPN1 0.8693226 0.0000000 protein tyrosine phosphatase non-receptor type 1 [Source:HGNC Symbol;Acc:HGNC:9642]
NFE2L2 1.1058788 0.0000000 NFE2 like bZIP transcription factor 2 [Source:HGNC Symbol;Acc:HGNC:7782]
ATF6 0.8184572 0.0000000 activating transcription factor 6 [Source:HGNC Symbol;Acc:HGNC:791]
HERPUD2 1.0629782 0.0000000 HERPUD family member 2 [Source:HGNC Symbol;Acc:HGNC:21915]
FICD -1.6827931 0.0000000 FIC domain protein adenylyltransferase [Source:HGNC Symbol;Acc:HGNC:18416]
CDK5RAP3 -1.0683387 0.0000000 CDK5 regulatory subunit associated protein 3 [Source:HGNC Symbol;Acc:HGNC:18673]
TMED2 0.8504556 0.0000000 transmembrane p24 trafficking protein 2 [Source:HGNC Symbol;Acc:HGNC:16996]
PDIA6 1.9605974 0.0000000 protein disulfide isomerase family A member 6 [Source:HGNC Symbol;Acc:HGNC:30168]
XBP1 0.6022125 0.0000000 X-box binding protein 1 [Source:HGNC Symbol;Acc:HGNC:12801]
STC2 1.4415016 0.0000000 stanniocalcin 2 [Source:HGNC Symbol;Acc:HGNC:11374]
OS9 -0.5082912 0.0000034 OS9 endoplasmic reticulum lectin [Source:HGNC Symbol;Acc:HGNC:16994]
DERL1 0.6513517 0.0000142 derlin 1 [Source:HGNC Symbol;Acc:HGNC:28454]
NCK1 0.9972591 0.0001843 NCK adaptor protein 1 [Source:HGNC Symbol;Acc:HGNC:7664]
PARP16 0.7732122 0.0004586 poly(ADP-ribose) polymerase family member 16 [Source:HGNC Symbol;Acc:HGNC:26040]
BAK1 0.8462247 0.0006944 BCL2 antagonist/killer 1 [Source:HGNC Symbol;Acc:HGNC:949]
ATF3 2.6025934 0.0006979 activating transcription factor 3 [Source:HGNC Symbol;Acc:HGNC:785]

Oxidoreductase activity GO:0016491

Highlight on the volcano plot of the genes found to be implicated in redox + table

gene log2FoldChange padj description
SQLE 1.9677248 0.0000000 squalene epoxidase [Source:HGNC Symbol;Acc:HGNC:11279]
P4HA1 2.1343453 0.0000000 prolyl 4-hydroxylase subunit alpha 1 [Source:HGNC Symbol;Acc:HGNC:8546]
FTH1 2.4058219 0.0000000 ferritin heavy chain 1 [Source:HGNC Symbol;Acc:HGNC:3976]
HSD17B12 1.7505653 0.0000000 hydroxysteroid 17-beta dehydrogenase 12 [Source:HGNC Symbol;Acc:HGNC:18646]
MTHFD2 1.5396345 0.0000000 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase [Source:HGNC Symbol;Acc:HGNC:7434]
NDUFB7 -1.4252231 0.0000000 NADH:ubiquinone oxidoreductase subunit B7 [Source:HGNC Symbol;Acc:HGNC:7702]
ETFB -1.4254615 0.0000000 electron transfer flavoprotein subunit beta [Source:HGNC Symbol;Acc:HGNC:3482]
HMGCR 1.4755899 0.0000000 3-hydroxy-3-methylglutaryl-CoA reductase [Source:HGNC Symbol;Acc:HGNC:5006]
OXR1 1.3412659 0.0000000 oxidation resistance 1 [Source:HGNC Symbol;Acc:HGNC:15822]
FADS2 1.1211500 0.0000000 fatty acid desaturase 2 [Source:HGNC Symbol;Acc:HGNC:3575]
NDUFS3 -1.0606974 0.0000000 NADH:ubiquinone oxidoreductase core subunit S3 [Source:HGNC Symbol;Acc:HGNC:7710]
DCXR -1.2800469 0.0000000 dicarbonyl and L-xylulose reductase [Source:HGNC Symbol;Acc:HGNC:18985]
PRDX3 1.8944825 0.0000000 peroxiredoxin 3 [Source:HGNC Symbol;Acc:HGNC:9354]
EGLN1 1.3891164 0.0000000 egl-9 family hypoxia inducible factor 1 [Source:HGNC Symbol;Acc:HGNC:1232]
KDM6A 1.5498310 0.0000000 lysine demethylase 6A [Source:HGNC Symbol;Acc:HGNC:12637]
SDHC 1.9322141 0.0000000 succinate dehydrogenase complex subunit C [Source:HGNC Symbol;Acc:HGNC:10682]
PGK1 0.8930287 0.0000000 phosphoglycerate kinase 1 [Source:HGNC Symbol;Acc:HGNC:8896]
KDM1A 1.1143569 0.0000000 lysine demethylase 1A [Source:HGNC Symbol;Acc:HGNC:29079]
ME2 0.9344287 0.0000000 malic enzyme 2 [Source:HGNC Symbol;Acc:HGNC:6984]
ETFA 1.0265180 0.0000000 electron transfer flavoprotein subunit alpha [Source:HGNC Symbol;Acc:HGNC:3481]
APEX1 1.1827315 0.0000000 apurinic/apyrimidinic endodeoxyribonuclease 1 [Source:HGNC Symbol;Acc:HGNC:587]
VKORC1 -1.1002662 0.0000000 vitamin K epoxide reductase complex subunit 1 [Source:HGNC Symbol;Acc:HGNC:23663]
GSTP1 -1.0910152 0.0000000 glutathione S-transferase pi 1 [Source:HGNC Symbol;Acc:HGNC:4638]
CTBP1 -1.0333567 0.0000000 C-terminal binding protein 1 [Source:HGNC Symbol;Acc:HGNC:2494]
CAT 1.4384963 0.0000000 catalase [Source:HGNC Symbol;Acc:HGNC:1516]
HIBADH 1.2310410 0.0000000 3-hydroxyisobutyrate dehydrogenase [Source:HGNC Symbol;Acc:HGNC:4907]
GAPDH 1.3157875 0.0000000 glyceraldehyde-3-phosphate dehydrogenase [Source:HGNC Symbol;Acc:HGNC:4141]
ALKBH6 -1.2975631 0.0000000 alkB homolog 6 [Source:HGNC Symbol;Acc:HGNC:28243]
DHRS4 -1.1106634 0.0000000 dehydrogenase/reductase 4 [Source:HGNC Symbol;Acc:HGNC:16985]
IDH3G -1.0185032 0.0000000 isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [Source:HGNC Symbol;Acc:HGNC:5386]
BLVRA -0.9486439 0.0000000 biliverdin reductase A [Source:HGNC Symbol;Acc:HGNC:1062]
NDUFV2 -0.7017629 0.0000000 NADH:ubiquinone oxidoreductase core subunit V2 [Source:HGNC Symbol;Acc:HGNC:7717]
MTRR 0.9186923 0.0000000 5-methyltetrahydrofolate-homocysteine methyltransferase reductase [Source:HGNC Symbol;Acc:HGNC:7473]
KDM8 -1.8486404 0.0000000 lysine demethylase 8 [Source:HGNC Symbol;Acc:HGNC:25840]
PRDX6 -0.7177835 0.0000000 peroxiredoxin 6 [Source:HGNC Symbol;Acc:HGNC:16753]
SUCLG2 1.4056385 0.0000000 succinate-CoA ligase GDP-forming subunit beta [Source:HGNC Symbol;Acc:HGNC:11450]
ALKBH2 -0.9275942 0.0000000 alkB homolog 2, alpha-ketoglutarate dependent dioxygenase [Source:HGNC Symbol;Acc:HGNC:32487]
ACADM 1.3279639 0.0000000 acyl-CoA dehydrogenase medium chain [Source:HGNC Symbol;Acc:HGNC:89]
TXNRD1 0.8457012 0.0000000 thioredoxin reductase 1 [Source:HGNC Symbol;Acc:HGNC:12437]
TET2 1.1333118 0.0000000 tet methylcytosine dioxygenase 2 [Source:HGNC Symbol;Acc:HGNC:25941]
COX6A1 -0.7093131 0.0000000 cytochrome c oxidase subunit 6A1 [Source:HGNC Symbol;Acc:HGNC:2277]
CYBA -0.8773041 0.0000000 cytochrome b-245 alpha chain [Source:HGNC Symbol;Acc:HGNC:2577]
FADS1 0.7865193 0.0000000 fatty acid desaturase 1 [Source:HGNC Symbol;Acc:HGNC:3574]
RSBN1 1.0267703 0.0000000 round spermatid basic protein 1 [Source:HGNC Symbol;Acc:HGNC:25642]
DOHH -1.0181291 0.0000000 deoxyhypusine hydroxylase [Source:HGNC Symbol;Acc:HGNC:28662]
MT-ND4 -1.2299276 0.0000000 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 [Source:HGNC Symbol;Acc:HGNC:7459]
DLAT 1.4189656 0.0000000 dihydrolipoamide S-acetyltransferase [Source:HGNC Symbol;Acc:HGNC:2896]
PRDX5 -0.7099264 0.0000000 peroxiredoxin 5 [Source:HGNC Symbol;Acc:HGNC:9355]
ALKBH4 -1.3700749 0.0000000 alkB homolog 4, lysine demethylase [Source:HGNC Symbol;Acc:HGNC:21900]
MT-CO3 -1.0495328 0.0000000 mitochondrially encoded cytochrome c oxidase III [Source:HGNC Symbol;Acc:HGNC:7422]
DHRS7 1.2230127 0.0000000 dehydrogenase/reductase 7 [Source:HGNC Symbol;Acc:HGNC:21524]
TXNL1 0.6806108 0.0000000 thioredoxin like 1 [Source:HGNC Symbol;Acc:HGNC:12436]
KDM1B 1.5109702 0.0000000 lysine demethylase 1B [Source:HGNC Symbol;Acc:HGNC:21577]
ENOX2 1.7889257 0.0000000 ecto-NOX disulfide-thiol exchanger 2 [Source:HGNC Symbol;Acc:HGNC:2259]
BCKDHB 1.3993568 0.0000000 branched chain keto acid dehydrogenase E1 subunit beta [Source:HGNC Symbol;Acc:HGNC:987]
PDIA6 1.9605974 0.0000000 protein disulfide isomerase family A member 6 [Source:HGNC Symbol;Acc:HGNC:30168]
ALDH16A1 -0.8634164 0.0000000 aldehyde dehydrogenase 16 family member A1 [Source:HGNC Symbol;Acc:HGNC:28114]
RRM2B 1.1083692 0.0000000 ribonucleotide reductase regulatory TP53 inducible subunit M2B [Source:HGNC Symbol;Acc:HGNC:17296]
HPDL -1.0528315 0.0000000 4-hydroxyphenylpyruvate dioxygenase like [Source:HGNC Symbol;Acc:HGNC:28242]
GFUS -0.9644788 0.0000000 GDP-L-fucose synthase [Source:HGNC Symbol;Acc:HGNC:12390]
TXNDC5 0.9816462 0.0000001 thioredoxin domain containing 5 [Source:HGNC Symbol;Acc:HGNC:21073]
MT-CO2 -1.0311870 0.0000001 mitochondrially encoded cytochrome c oxidase II [Source:HGNC Symbol;Acc:HGNC:7421]
L2HGDH 1.0615049 0.0000001 L-2-hydroxyglutarate dehydrogenase [Source:HGNC Symbol;Acc:HGNC:20499]
MSRB3 0.7589829 0.0000001 methionine sulfoxide reductase B3 [Source:HGNC Symbol;Acc:HGNC:27375]
NDUFS8 -0.8497261 0.0000001 NADH:ubiquinone oxidoreductase core subunit S8 [Source:HGNC Symbol;Acc:HGNC:7715]
ALDH6A1 1.0998006 0.0000002 aldehyde dehydrogenase 6 family member A1 [Source:HGNC Symbol;Acc:HGNC:7179]
KDSR 0.5683562 0.0000005 3-ketodihydrosphingosine reductase [Source:HGNC Symbol;Acc:HGNC:4021]
ACADVL -0.6128132 0.0000005 acyl-CoA dehydrogenase very long chain [Source:HGNC Symbol;Acc:HGNC:92]
MGST2 -0.8752367 0.0000006 microsomal glutathione S-transferase 2 [Source:HGNC Symbol;Acc:HGNC:7063]
PCBD2 -0.8282777 0.0000006 pterin-4 alpha-carbinolamine dehydratase 2 [Source:HGNC Symbol;Acc:HGNC:24474]
COX5A 1.0745872 0.0000007 cytochrome c oxidase subunit 5A [Source:HGNC Symbol;Acc:HGNC:2267]
RIOX1 -0.9372983 0.0000011 ribosomal oxygenase 1 [Source:HGNC Symbol;Acc:HGNC:20968]
NDUFA2 -1.1354351 0.0000012 NADH:ubiquinone oxidoreductase subunit A2 [Source:HGNC Symbol;Acc:HGNC:7685]
ALDH1B1 -0.8223101 0.0000018 aldehyde dehydrogenase 1 family member B1 [Source:HGNC Symbol;Acc:HGNC:407]
GPX4 -0.5629846 0.0000018 glutathione peroxidase 4 [Source:HGNC Symbol;Acc:HGNC:4556]
AOC3 2.0065628 0.0000019 amine oxidase copper containing 3 [Source:HGNC Symbol;Acc:HGNC:550]
SC5D 0.7047703 0.0000036 sterol-C5-desaturase [Source:HGNC Symbol;Acc:HGNC:10547]
NDUFV1 -0.5988942 0.0000039 NADH:ubiquinone oxidoreductase core subunit V1 [Source:HGNC Symbol;Acc:HGNC:7716]
COX7A2 0.8957250 0.0000046 cytochrome c oxidase subunit 7A2 [Source:HGNC Symbol;Acc:HGNC:2288]
DUS1L -0.5876339 0.0000068 dihydrouridine synthase 1 like [Source:HGNC Symbol;Acc:HGNC:30086]
OGDH 0.8376095 0.0000075 oxoglutarate dehydrogenase [Source:HGNC Symbol;Acc:HGNC:8124]
AKR1A1 -0.5929624 0.0000081 aldo-keto reductase family 1 member A1 [Source:HGNC Symbol;Acc:HGNC:380]
LPO -1.1346622 0.0000082 lactoperoxidase [Source:HGNC Symbol;Acc:HGNC:6678]
MT-ND3 -1.3941667 0.0000089 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 3 [Source:HGNC Symbol;Acc:HGNC:7458]
FXN -0.8011508 0.0000124 frataxin [Source:HGNC Symbol;Acc:HGNC:3951]
CCS -0.8888991 0.0000129 copper chaperone for superoxide dismutase [Source:HGNC Symbol;Acc:HGNC:1613]
SESN3 0.7335457 0.0000131 sestrin 3 [Source:HGNC Symbol;Acc:HGNC:23060]
CYB5R3 -0.5519597 0.0000134 cytochrome b5 reductase 3 [Source:HGNC Symbol;Acc:HGNC:2873]
DLD 0.8008823 0.0000152 dihydrolipoamide dehydrogenase [Source:HGNC Symbol;Acc:HGNC:2898]
DHRS1 -0.8491679 0.0000158 dehydrogenase/reductase 1 [Source:HGNC Symbol;Acc:HGNC:16445]
ALOX5AP -0.8279202 0.0000177 arachidonate 5-lipoxygenase activating protein [Source:HGNC Symbol;Acc:HGNC:436]
ALDH18A1 0.8368068 0.0000201 aldehyde dehydrogenase 18 family member A1 [Source:HGNC Symbol;Acc:HGNC:9722]
HADHA 0.7045755 0.0000206 hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha [Source:HGNC Symbol;Acc:HGNC:4801]
BCKDHA 0.7519168 0.0000312 branched chain keto acid dehydrogenase E1 subunit alpha [Source:HGNC Symbol;Acc:HGNC:986]
EGLN2 -0.6494318 0.0000350 egl-9 family hypoxia inducible factor 2 [Source:HGNC Symbol;Acc:HGNC:14660]
COIL 0.6092529 0.0000397 coilin [Source:HGNC Symbol;Acc:HGNC:2184]
DHCR7 0.5519582 0.0000498 7-dehydrocholesterol reductase [Source:HGNC Symbol;Acc:HGNC:2860]
IDH3A 1.2514687 0.0000540 isocitrate dehydrogenase (NAD(+)) 3 catalytic subunit alpha [Source:HGNC Symbol;Acc:HGNC:5384]
CYB5R4 0.7556952 0.0000573 cytochrome b5 reductase 4 [Source:HGNC Symbol;Acc:HGNC:20147]
IMPDH1 -0.5191490 0.0000576 inosine monophosphate dehydrogenase 1 [Source:HGNC Symbol;Acc:HGNC:6052]
FOXRED1 -0.5894753 0.0000698 FAD dependent oxidoreductase domain containing 1 [Source:HGNC Symbol;Acc:HGNC:26927]
TMX1 0.6256027 0.0000754 thioredoxin related transmembrane protein 1 [Source:HGNC Symbol;Acc:HGNC:15487]
PTGS2 2.0092889 0.0000952 prostaglandin-endoperoxide synthase 2 [Source:HGNC Symbol;Acc:HGNC:9605]
PARK7 -0.5136427 0.0001046 Parkinsonism associated deglycase [Source:HGNC Symbol;Acc:HGNC:16369]
TET3 0.5851921 0.0001160 tet methylcytosine dioxygenase 3 [Source:HGNC Symbol;Acc:HGNC:28313]
SELENOT 0.8098330 0.0001181 selenoprotein T [Source:HGNC Symbol;Acc:HGNC:18136]
FTO 0.7890898 0.0001341 FTO alpha-ketoglutarate dependent dioxygenase [Source:HGNC Symbol;Acc:HGNC:24678]
IVD -0.4533351 0.0001650 isovaleryl-CoA dehydrogenase [Source:HGNC Symbol;Acc:HGNC:6186]
SELENOW -0.8970265 0.0001777 selenoprotein W [Source:HGNC Symbol;Acc:HGNC:10752]
ALDH1L2 0.7364999 0.0001866 aldehyde dehydrogenase 1 family member L2 [Source:HGNC Symbol;Acc:HGNC:26777]
CYB5B 0.4770099 0.0002536 cytochrome b5 type B [Source:HGNC Symbol;Acc:HGNC:24374]
P4HB 0.4206141 0.0003121 prolyl 4-hydroxylase subunit beta [Source:HGNC Symbol;Acc:HGNC:8548]
ME3 -0.8628819 0.0003375 malic enzyme 3 [Source:HGNC Symbol;Acc:HGNC:6985]
GPX1 0.7188221 0.0003640 glutathione peroxidase 1 [Source:HGNC Symbol;Acc:HGNC:4553]
NQO2 -0.6846379 0.0003721 N-ribosyldihydronicotinamide:quinone reductase 2 [Source:HGNC Symbol;Acc:HGNC:7856]
SDHD 0.8619113 0.0003789 succinate dehydrogenase complex subunit D [Source:HGNC Symbol;Acc:HGNC:10683]
TECR -0.4875875 0.0003948 trans-2,3-enoyl-CoA reductase [Source:HGNC Symbol;Acc:HGNC:4551]
UEVLD 0.9680126 0.0003956 UEV and lactate/malate dehyrogenase domains [Source:HGNC Symbol;Acc:HGNC:30866]
AOC2 1.5651702 0.0003973 amine oxidase copper containing 2 [Source:HGNC Symbol;Acc:HGNC:549]
MT-ND4L -1.2284198 0.0004218 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4L [Source:HGNC Symbol;Acc:HGNC:7460]
CYP1B1 0.7015293 0.0005418 cytochrome P450 family 1 subfamily B member 1 [Source:HGNC Symbol;Acc:HGNC:2597]
MT-ND1 -1.0988021 0.0005471 mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 [Source:HGNC Symbol;Acc:HGNC:7455]
ACADSB 0.6701509 0.0005597 acyl-CoA dehydrogenase short/branched chain [Source:HGNC Symbol;Acc:HGNC:91]
DUS2 -0.6944042 0.0006011 dihydrouridine synthase 2 [Source:HGNC Symbol;Acc:HGNC:26014]
DPYD 1.0109534 0.0006067 dihydropyrimidine dehydrogenase [Source:HGNC Symbol;Acc:HGNC:3012]
FASN 0.4674484 0.0007743 fatty acid synthase [Source:HGNC Symbol;Acc:HGNC:3594]
KDM4C 0.5855580 0.0008278 lysine demethylase 4C [Source:HGNC Symbol;Acc:HGNC:17071]
HADH 0.4948329 0.0008947 hydroxyacyl-CoA dehydrogenase [Source:HGNC Symbol;Acc:HGNC:4799]
FDX2 -1.0580009 0.0009679 ferredoxin 2 [Source:HGNC Symbol;Acc:HGNC:30546]

Crossing with immunopeptidomic data

Table of the genes that could be found as proteins in the significantly enriched peptides in the immunopeptidomic data.

## [1] 44 13
gene log2FoldChange padj description
KRTCAP2 -1.5021573 0.0000000 keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:HGNC:28942]
PRTN3 -1.2107807 0.0000000 proteinase 3 [Source:HGNC Symbol;Acc:HGNC:9495]
METAP2 1.1040167 0.0000000 methionyl aminopeptidase 2 [Source:HGNC Symbol;Acc:HGNC:16672]
TFRC 1.3851207 0.0000000 transferrin receptor [Source:HGNC Symbol;Acc:HGNC:11763]
RPL35 -1.1732016 0.0000000 ribosomal protein L35 [Source:HGNC Symbol;Acc:HGNC:10344]
ELANE -1.2322149 0.0000000 elastase, neutrophil expressed [Source:HGNC Symbol;Acc:HGNC:3309]
PXK 1.1528337 0.0000000 PX domain containing serine/threonine kinase like [Source:HGNC Symbol;Acc:HGNC:23326]
RBMX 0.9197177 0.0000000 RNA binding motif protein X-linked [Source:HGNC Symbol;Acc:HGNC:9910]
ARCN1 1.1220940 0.0000000 archain 1 [Source:HGNC Symbol;Acc:HGNC:649]
PPP1R27 -1.4553395 0.0000000 protein phosphatase 1 regulatory subunit 27 [Source:HGNC Symbol;Acc:HGNC:16813]
PMF1 -0.8998079 0.0000000 polyamine modulated factor 1 [Source:HGNC Symbol;Acc:HGNC:9112]
ATP5PF -0.9758286 0.0000000 ATP synthase peripheral stalk subunit F6 [Source:HGNC Symbol;Acc:HGNC:847]
FLI1 1.4676177 0.0000000 Fli-1 proto-oncogene, ETS transcription factor [Source:HGNC Symbol;Acc:HGNC:3749]
TSTD2 2.0711363 0.0000000 thiosulfate sulfurtransferase like domain containing 2 [Source:HGNC Symbol;Acc:HGNC:30087]
RPS10 -1.1709501 0.0000000 ribosomal protein S10 [Source:HGNC Symbol;Acc:HGNC:10383]
TGS1 1.1872364 0.0000000 trimethylguanosine synthase 1 [Source:HGNC Symbol;Acc:HGNC:17843]
PRPF31 -0.9557415 0.0000000 pre-mRNA processing factor 31 [Source:HGNC Symbol;Acc:HGNC:15446]
TXNIP 1.2337513 0.0000000 thioredoxin interacting protein [Source:HGNC Symbol;Acc:HGNC:16952]
DNAJA2 1.0801674 0.0000000 DnaJ heat shock protein family (Hsp40) member A2 [Source:HGNC Symbol;Acc:HGNC:14884]
BCLAF1 0.6766773 0.0000000 BCL2 associated transcription factor 1 [Source:HGNC Symbol;Acc:HGNC:16863]
RPS17 -0.7267731 0.0000000 ribosomal protein S17 [Source:HGNC Symbol;Acc:HGNC:10397]
TRIM13 -0.7992741 0.0000000 tripartite motif containing 13 [Source:HGNC Symbol;Acc:HGNC:9976]
NME3 -1.3097075 0.0000000 NME/NM23 nucleoside diphosphate kinase 3 [Source:HGNC Symbol;Acc:HGNC:7851]
LNPEP 1.1727759 0.0000000 leucyl and cystinyl aminopeptidase [Source:HGNC Symbol;Acc:HGNC:6656]
MTA2 -0.7637732 0.0000000 metastasis associated 1 family member 2 [Source:HGNC Symbol;Acc:HGNC:7411]
RPL34 -0.7593908 0.0000000 ribosomal protein L34 [Source:HGNC Symbol;Acc:HGNC:10340]
CD46 0.6964974 0.0000001 CD46 molecule [Source:HGNC Symbol;Acc:HGNC:6953]
B2M 0.8496441 0.0000001 beta-2-microglobulin [Source:HGNC Symbol;Acc:HGNC:914]
PPT1 1.1207877 0.0000003 palmitoyl-protein thioesterase 1 [Source:HGNC Symbol;Acc:HGNC:9325]
ATP5F1B 0.8913198 0.0000003 ATP synthase F1 subunit beta [Source:HGNC Symbol;Acc:HGNC:830]
TUBB4B -0.8346326 0.0000007 tubulin beta 4B class IVb [Source:HGNC Symbol;Acc:HGNC:20771]
ABHD17B 0.8712265 0.0000041 abhydrolase domain containing 17B, depalmitoylase [Source:HGNC Symbol;Acc:HGNC:24278]
HNRNPF 0.7953479 0.0000121 heterogeneous nuclear ribonucleoprotein F [Source:HGNC Symbol;Acc:HGNC:5039]
METAP1 0.5845978 0.0000131 methionyl aminopeptidase 1 [Source:HGNC Symbol;Acc:HGNC:15789]
PAPOLA 0.5077699 0.0000167 poly(A) polymerase alpha [Source:HGNC Symbol;Acc:HGNC:14981]
GFPT1 0.7942751 0.0000173 glutamine–fructose-6-phosphate transaminase 1 [Source:HGNC Symbol;Acc:HGNC:4241]
HUWE1 0.4493750 0.0001868 HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 [Source:HGNC Symbol;Acc:HGNC:30892]
CIRBP -0.4092358 0.0002673 cold inducible RNA binding protein [Source:HGNC Symbol;Acc:HGNC:1982]
COPZ1 -0.4227278 0.0003366 COPI coat complex subunit zeta 1 [Source:HGNC Symbol;Acc:HGNC:2243]
CAD -0.5876069 0.0003795 carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase [Source:HGNC Symbol;Acc:HGNC:1424]
CDK17 0.6835569 0.0005126 cyclin dependent kinase 17 [Source:HGNC Symbol;Acc:HGNC:8750]
FASN 0.4674484 0.0007743 fatty acid synthase [Source:HGNC Symbol;Acc:HGNC:3594]
PSMD7 0.5346745 0.0008086 proteasome 26S subunit, non-ATPase 7 [Source:HGNC Symbol;Acc:HGNC:9565]
HNRNPDL 0.3766856 0.0009490 heterogeneous nuclear ribonucleoprotein D like [Source:HGNC Symbol;Acc:HGNC:5037]

Crossing with the proteomics data

## [1] 21 13
gene log2FoldChange padj description
CD63 -1.0314250 0.0000000 CD63 molecule [Source:HGNC Symbol;Acc:HGNC:1692]
LMAN1 1.1586409 0.0000000 lectin, mannose binding 1 [Source:HGNC Symbol;Acc:HGNC:6631]
SRGN 1.0732210 0.0000000 serglycin [Source:HGNC Symbol;Acc:HGNC:9361]
ERP29 -0.7739467 0.0000000 endoplasmic reticulum protein 29 [Source:HGNC Symbol;Acc:HGNC:13799]
FDFT1 0.8132262 0.0000000 farnesyl-diphosphate farnesyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:3629]
PSAP 0.9303391 0.0000000 prosaposin [Source:HGNC Symbol;Acc:HGNC:9498]
SEPTIN6 0.8225595 0.0000000 septin 6 [Source:HGNC Symbol;Acc:HGNC:15848]
CRELD2 -0.7833789 0.0000000 cysteine rich with EGF like domains 2 [Source:HGNC Symbol;Acc:HGNC:28150]
TMED2 0.8504556 0.0000000 transmembrane p24 trafficking protein 2 [Source:HGNC Symbol;Acc:HGNC:16996]
HYOU1 1.0856251 0.0000001 hypoxia up-regulated 1 [Source:HGNC Symbol;Acc:HGNC:16931]
SSR1 0.6722112 0.0000002 signal sequence receptor subunit 1 [Source:HGNC Symbol;Acc:HGNC:11323]
HLA-A -0.8742236 0.0000003 major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:HGNC:4931]
CTDSPL2 0.8425381 0.0000021 CTD small phosphatase like 2 [Source:HGNC Symbol;Acc:HGNC:26936]
LIPA 1.1072755 0.0000054 lipase A, lysosomal acid type [Source:HGNC Symbol;Acc:HGNC:6617]
NOMO3 1.7667326 0.0000194 NODAL modulator 3 [Source:HGNC Symbol;Acc:HGNC:25242]
DHX34 -0.6251980 0.0000320 DExH-box helicase 34 [Source:HGNC Symbol;Acc:HGNC:16719]
RPL26 -0.5912310 0.0000644 ribosomal protein L26 [Source:HGNC Symbol;Acc:HGNC:10327]
ALDH1L2 0.7364999 0.0001866 aldehyde dehydrogenase 1 family member L2 [Source:HGNC Symbol;Acc:HGNC:26777]
BCAP31 -0.4427626 0.0002662 B cell receptor associated protein 31 [Source:HGNC Symbol;Acc:HGNC:16695]
GNS 0.6935357 0.0004480 glucosamine (N-acetyl)-6-sulfatase [Source:HGNC Symbol;Acc:HGNC:4422]
CTSA -0.5690985 0.0007756 cathepsin A [Source:HGNC Symbol;Acc:HGNC:9251]

Save the data and the environment

Session info

sessionInfo()
## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19045)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_Belgium.utf8  LC_CTYPE=English_Belgium.utf8   
## [3] LC_MONETARY=English_Belgium.utf8 LC_NUMERIC=C                    
## [5] LC_TIME=English_Belgium.utf8    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] readxl_1.4.1          msigdbr_7.5.1         clusterProfiler_4.6.0
##  [4] ggrepel_0.9.2         forcats_0.5.2         stringr_1.4.1        
##  [7] dplyr_1.0.10          purrr_0.3.5           readr_2.1.3          
## [10] tidyr_1.2.1           tibble_3.1.8          ggplot2_3.4.0        
## [13] tidyverse_1.3.2      
## 
## loaded via a namespace (and not attached):
##   [1] snow_0.4-4             shadowtext_0.1.2       backports_1.4.1       
##   [4] fastmatch_1.1-3        plyr_1.8.8             igraph_1.3.5          
##   [7] lazyeval_0.2.2         splines_4.2.2          BiocParallel_1.32.4   
##  [10] GenomeInfoDb_1.34.4    digest_0.6.30          yulab.utils_0.0.6     
##  [13] htmltools_0.5.3        GOSemSim_2.24.0        viridis_0.6.2         
##  [16] GO.db_3.16.0           fansi_1.0.3            magrittr_2.0.3        
##  [19] memoise_2.0.1          googlesheets4_1.0.1    tzdb_0.3.0            
##  [22] Biostrings_2.66.0      graphlayouts_0.8.4     modelr_0.1.10         
##  [25] vroom_1.6.0            timechange_0.1.1       enrichplot_1.18.3     
##  [28] colorspace_2.0-3       blob_1.2.3             rvest_1.0.3           
##  [31] haven_2.5.2            xfun_0.34              crayon_1.5.2          
##  [34] RCurl_1.98-1.9         jsonlite_1.8.3         scatterpie_0.1.8      
##  [37] ape_5.6-2              glue_1.6.2             polyclip_1.10-4       
##  [40] gtable_0.3.1           gargle_1.2.1           zlibbioc_1.44.0       
##  [43] XVector_0.38.0         BiocGenerics_0.44.0    scales_1.2.1          
##  [46] DOSE_3.24.2            DBI_1.1.3              Rcpp_1.0.9            
##  [49] viridisLite_0.4.1      gridGraphics_0.5-1     tidytree_0.4.2        
##  [52] bit_4.0.4              stats4_4.2.2           httr_1.4.4            
##  [55] fgsea_1.24.0           RColorBrewer_1.1-3     ellipsis_0.3.2        
##  [58] pkgconfig_2.0.3        farver_2.1.1           sass_0.4.2            
##  [61] dbplyr_2.2.1           utf8_1.2.2             labeling_0.4.2        
##  [64] ggplotify_0.1.0        tidyselect_1.2.0       rlang_1.0.6           
##  [67] reshape2_1.4.4         AnnotationDbi_1.60.0   munsell_0.5.0         
##  [70] cellranger_1.1.0       tools_4.2.2            cachem_1.0.6          
##  [73] downloader_0.4         cli_3.4.1              generics_0.1.3        
##  [76] RSQLite_2.2.19         gson_0.0.9             broom_1.0.1           
##  [79] evaluate_0.18          fastmap_1.1.0          yaml_2.3.6            
##  [82] ggtree_3.6.2           babelgene_22.9         knitr_1.41            
##  [85] bit64_4.0.5            fs_1.5.2               tidygraph_1.2.2       
##  [88] KEGGREST_1.38.0        ggraph_2.1.0           nlme_3.1-160          
##  [91] aplot_0.1.9            xml2_1.3.3             compiler_4.2.2        
##  [94] rstudioapi_0.14        png_0.1-7              reprex_2.0.2          
##  [97] treeio_1.22.0          tweenr_2.0.2           bslib_0.4.1           
## [100] stringi_1.7.8          highr_0.9              lattice_0.20-45       
## [103] Matrix_1.5-1           vctrs_0.5.0            pillar_1.8.1          
## [106] lifecycle_1.0.3        jquerylib_0.1.4        data.table_1.14.4     
## [109] cowplot_1.1.1          bitops_1.0-7           patchwork_1.1.2       
## [112] qvalue_2.30.0          R6_2.5.1               gridExtra_2.3         
## [115] IRanges_2.32.0         codetools_0.2-18       MASS_7.3-58.1         
## [118] assertthat_0.2.1       withr_2.5.0            S4Vectors_0.36.0      
## [121] GenomeInfoDbData_1.2.9 parallel_4.2.2         hms_1.1.2             
## [124] grid_4.2.2             ggfun_0.0.9            HDO.db_0.99.1         
## [127] rmarkdown_2.18         googledrive_2.0.0      ggnewscale_0.4.8      
## [130] ggforce_0.4.1          Biobase_2.58.0         lubridate_1.9.0